Abstract In this study, the interaction of an alkylating agent, sulfur mustard (SM) with rat liver active (S 1 and S 2) and inactive (P 2) chromatin was investigated employing UV/vis spectroscopy and gel electrophoreses. The results show that SM affects the chromatin structure in a dose-dependent manner. The binding of SM to fractions is different. At lower concentrations (<500 μM), SM seems to unfold the structure and at higher concentrations, it induces aggregation and condensation of chromatin possibly via forming cross-links between the chromatin components. The extent of condensation in S 2 is higher when compared to the P 2 fraction.